Contacts of the helix formed by residues 275 - 289 (chain C) in PDB entry 4OGB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 275 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227C SER* 3.6 24.4 + - - -
269C LEU* 3.3 25.6 - - - +
270C ALA* 4.5 7.4 - - - +
272C ASP* 2.9 14.5 + - + +
274C SER* 1.3 87.6 + - - +
276C HIS* 1.3 61.8 + - - +
277C MET 3.5 1.8 - - - -
278C ASN* 3.5 12.6 + - + +
279C LEU* 3.0 26.4 + - + +
508C EDO 3.5 34.2 - - - +
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Residues in contact with HIS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ALA 6.0 0.2 - - - -
272C ASP 4.0 1.0 + - - -
273C MET* 3.2 31.5 + - + +
274C SER 3.4 0.6 - - - -
275C LYS* 1.3 77.2 - - - +
277C MET* 1.3 88.8 + - + +
279C LEU* 3.1 6.2 + - - +
280C LEU* 2.9 43.0 + - + +
315C HIS* 2.9 36.5 + + + +
375C TYR 4.6 1.4 + - - -
376C ILE* 3.9 49.5 - - + +
380C LEU* 4.2 14.6 - - + -
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Residues in contact with MET 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C SER 5.2 3.5 + - - +
275C LYS 3.5 0.6 - - - -
276C HIS* 1.3 96.0 - - + +
278C ASN* 1.3 60.0 + - - +
280C LEU* 3.4 8.3 + - - +
281C ALA* 2.8 37.1 + - - +
375C TYR 5.4 2.5 - - - +
376C ILE* 4.8 13.7 - - + -
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Residues in contact with ASN 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C SER 4.9 9.7 + - - -
275C LYS* 3.5 11.3 + - + +
276C HIS 3.2 0.8 - - - -
277C MET* 1.3 78.0 - - - +
279C LEU* 1.3 65.8 + - - +
281C ALA* 4.1 5.4 - - - +
282C ASP* 3.1 31.9 + - - +
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ALA* 3.7 34.1 - - + +
275C LYS* 3.0 17.2 + - + +
276C HIS* 3.4 9.0 - - - +
278C ASN* 1.3 76.7 - - - +
280C LEU* 1.3 52.9 + - - +
282C ASP* 3.3 5.3 + - + +
283C LEU* 2.8 33.3 + - - +
308C GLN* 5.5 3.1 - - + -
311C GLN* 4.1 28.0 - - + +
312C ASN* 3.7 29.4 + - - +
315C HIS* 3.7 32.3 - - + +
508C EDO 5.4 4.3 - - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C HIS* 2.9 42.4 + - + +
277C MET* 3.6 8.7 - - - +
279C LEU* 1.3 74.2 - - - +
281C ALA* 1.3 55.3 - - - +
283C LEU* 2.9 7.1 + - + +
284C LYS* 2.8 54.5 + - - +
312C ASN* 4.2 2.2 + - - -
315C HIS* 5.9 0.2 - - - -
375C TYR 5.8 0.7 - - - +
379C PRO* 3.8 29.2 - - + +
380C LEU* 3.9 17.9 - - + +
383C THR* 3.5 32.1 - - + +
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Residues in contact with ALA 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C MET 2.8 22.5 + - - +
278C ASN* 4.1 8.1 - - - +
280C LEU* 1.3 71.8 - - - +
282C ASP* 1.3 64.7 + - - +
284C LYS* 3.4 14.2 + - - +
285C THR* 3.1 25.1 + - - -
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Residues in contact with ASP 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ASN* 3.1 23.0 + - - +
279C LEU* 3.5 6.5 - - + +
281C ALA* 1.3 77.5 - - - +
283C LEU* 1.3 62.9 + - - +
285C THR* 3.3 9.9 + - - +
286C MET 3.1 14.9 + - - -
308C GLN* 2.7 35.6 + - + +
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU 2.8 14.0 + - - +
280C LEU* 2.9 9.4 + - + +
282C ASP* 1.3 74.2 - - - +
284C LYS* 1.3 65.3 + - - +
286C MET* 3.2 17.7 + - - +
287C VAL* 3.0 23.8 + - + +
308C GLN* 3.7 5.3 - - - +
309C VAL* 5.4 1.6 - - - -
312C ASN* 3.7 37.5 - - + +
380C LEU* 4.5 11.4 - - + -
383C THR* 3.7 23.1 - - + -
384C TRP* 4.0 23.8 - - + +
387C LEU* 4.1 23.1 - - + -
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Residues in contact with LYS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 2.8 38.2 + - + +
281C ALA* 3.6 13.7 - - - +
282C ASP 3.3 0.2 - - - -
283C LEU* 1.3 75.4 - - - +
285C THR* 1.3 61.0 + - - +
287C VAL* 3.3 6.3 + - - +
288C GLU* 3.2 27.8 + - + +
379C PRO* 4.8 8.9 - - - +
383C THR* 3.6 33.4 - - + +
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Residues in contact with THR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ALA 3.1 14.9 + - - -
282C ASP* 3.5 12.9 + - - -
283C LEU 3.2 0.4 - - - -
284C LYS* 1.3 73.2 - - - +
286C MET* 1.3 65.8 + - - +
288C GLU* 3.3 9.0 + - + +
289C THR* 3.3 27.3 + - - +
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Residues in contact with MET 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ASP 3.1 13.1 + - - +
283C LEU* 3.5 16.2 - - - +
285C THR* 1.3 74.4 - - - +
287C VAL* 1.3 64.9 + - - +
289C THR* 3.4 5.4 + - - +
290C LYS* 3.1 23.5 + - - +
298C LEU* 5.9 1.6 - - + -
300C LEU* 4.5 9.0 - - + -
305C ASP* 3.2 50.5 - - + +
308C GLN* 3.2 26.0 - - - +
309C VAL* 3.5 26.0 - - - -
387C LEU* 3.9 17.7 - - + -
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 3.0 18.8 + - + +
284C LYS* 3.4 10.5 - - - +
285C THR 3.2 0.2 - - - -
286C MET* 1.3 78.5 - - - +
288C GLU* 1.3 66.7 - - - +
290C LYS* 3.2 22.2 - - + +
383C THR* 3.6 31.4 - - + +
386C ASP* 4.2 23.6 - - + +
387C LEU* 3.8 23.8 - - + +
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Residues in contact with GLU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LYS 3.2 16.1 + - - +
285C THR* 3.3 11.1 + - + +
287C VAL* 1.3 82.2 - - - +
289C THR* 1.3 58.9 + - - +
290C LYS 3.3 2.5 + - - -
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Residues in contact with THR 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C THR* 3.3 21.2 + - - +
286C MET* 3.6 7.0 - - - -
287C VAL 3.3 0.2 - - - -
288C GLU* 1.3 78.8 - - - +
290C LYS* 1.3 64.8 + - - +
291C LYS* 3.4 31.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il